Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA Sequencing analysis of transcriptomics to investigate the bile stress response in L. paracasei L9

ABSTRACT: Purpose: To understand the bile salts resistance mechanisms in L. paracasei L9 Methods: Samples from L9 cultured with or without bile salts were sequenced on an Illumina Hiseq platform. Three independent biological replicates were produced including 6 samples in total. Results: Raw data were firstly processed through in-house perl scripts to generate clean data, and then clean date were mapped to the reference genome, getting about 8-10 million total mapped reads per sample.

ORGANISM(S): Lacticaseibacillus paracasei

PROVIDER: GSE108713 | GEO | 2018/01/17

SECONDARY ACCESSION(S): PRJNA428354

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Global transcriptional responses to a long-term treatment of bile salts in Bifidobacterium longum BBMN68

Project description:Purpose：Bifidobacteria are common inhabitants of the human gastrointestinal tract. In order to colonize in the gut, it is important to adapt to the physiological concentrations of bile salts. The global response to bile in B. longum BBMN68, isolated from a healthy centenarian in the Bama County of the Guangxi Zhuang Autonomous Region in China, has been investigated through RNA-seq transcriptomics sequencing in our previous work. However, a long-term bile salts treatment is more suitable to simulate the human gastrointestinal tract environment. The goals of this study are to invstigated the global response to a long-term treatment of bile salts in B. longum BBMN68. Methods: Samples from BBMN68 cultured with or without 0.75 g liter-1 ox-bile for 24 hours were sequenced on an Illumina Hiseq platform. Three independent biological replicates were produced including 6 samples in total. Results: Raw data were firstly processed through in-house perl scripts to generate clean data, and then clean date were mapped to the reference genome, getting about 11-13 million total mapped reads per sample.

2018-05-04 | GSE113993 | GEO

RNA sequencing analysis of transcriptomics to study the growth of Lactobacillus salivarius Ren in raffinose

Project description:Purpose: To understand the metabolic mechanism of Lactobacillus salivarius Ren in raffinose Methods: Samples of Lactobacillus salivarius Ren grown in glucose and raffinose were sequenced on the Illumina Hiseq platform. Three independent biological replicates were generated, including a total of six samples. Results: Raw data were firstly processed through in-house perl scripts to generate clean data, and then clean date were mapped to the reference genome, getting about 8-10 million total mapped reads per sample.

2018-11-14 | GSE122483 | GEO

Differential microRNA expression and microRNA editing upon HP-PRRSV infection in vivo across different pig breeds

Project description:Purpose: To characterize the differential microRNA expression profiles and microRNA editing upon PRRSV infection, using NGS techonology, we sequenced small RNAs of the lungs of Tongcheng and Landrace pigs before (0 dpi) and after (3, 5, 7 dpi) infection with high-pathogenic PRRSV (HP-PRRSV). Methods: The miRNA expression profiles of the lungs of Tongcheng and Landrace pigs before (0 dpi) and after (3, 5, 7 dpi) HP-PRRSV infection were produced by using solexa platform. The raw reads with low qualities were filtered and the clean high quality reads were mapped to Ensembl Sus reference genome 10.2.71 using BWA. The unique mapped reads were retained for microRNA expression analysis. The raw reads counts of each microRNA were calculated by perl scripts and the differentially expressed microRNA (Fold change >2; FDR <0.05) were called using edgeR. The microRNA editing was identified using the methods described by Alon, S. and E. Eisenberg. Methods Mol Biol, 2013. Further analysis of microRNA editing was performed with perl scripts.

2014-10-10 | GSE58436 | GEO

RNA Sequencing analysis of transcriptomics to investigate the bile stress response in L. paracasei L9

Project description:RNA Sequencing analysis of transcriptomics to investigate the bile stress response in L. paracasei L9

| PRJNA428354 | ENA

Bile Salts Enhance the Susceptibility of the Allergenic Lipid Transfer Protein from Peach, Pru p 3 to in vitro gastrointestinal digestion

Project description:Sensitisation to the lipid transfer protein Pru p 3 is associated with severe allergic reactions to peach, the proteins stability being thought to play a role in its allergenicity. Lipid binding increases susceptibility of Pru p 3 to digestion and so the impact of bile salts on the in vitro gastrointestinal digestibility of Pru p 3 was investigated and digestion products mapped by SDS PAGE and mass spectrometry. Bile salts enhanced the digestibility of Prup3 resulting in an ensemble of around 100 peptides spanning the proteins sequence which were linked by disulphide bonds into structures of ~5-6kDa. IgE binding studies with a serum panel from peach allergic subjects showed digestion reduced, but did not abolish, the IgE reactivity of Pru p 3. These data show the importance of including bile salts in in vitro digestion systems and emphasise the need to profile of digestion in a manner that allows identification of immunologically relevant disulphide-linked peptide aggregates.

2023-10-24 | PXD037801 | Pride

Gene expression of Vibrio parahaemolyticus growing in laboratory isolation conditions compared to those common in its natural ocean environment

Project description:Using high-throughput sequencing of RNA obtained from triplicate samples, we compared the differential gene expression of V. parahaemolyticus when growing at 37°C, 0.9% NaCl, and 0.04% bile salts with that at 12°C, 3% NaCl without bile salts, a condition similar to that prevailing in the ocean.

2017-06-09 | GSE92847 | GEO

RNA-seq of 10-day-old Arabidopsis seedlings of Col-0, cpl3 mutant, and pentuple-della mutant genotype

Project description:C-TERMINAL DOMAIN PHOSPHATASE-LIKE 3 (CPL3) is a phosphatase that interacts with the DELLA proteins RGA and GAI, promoting their function. We examined whether CPL3 is involved in regulating the activity of DELLAs, in particular regarding their function in controlling gene expression. For this purpose, we profiled the transcriptome of the cpl3-3 mutant and compared it with that of the dellap (pentuple della) mutant in the same conditions. 10-day-old plants were used to extract RNA with the miRNeasy Mini Kit (Qiagen). The RNAs were first selected via enrichment of their poly(A) tail and then further fragmented into 300~350 bp fragments to build the libraries. Then, the libraries were sequenced on BGIseq500 platform (BGI, Shenzhen, China), the raw data of FASTQ format were firstly processed through in-house Perl scripts. Next, clean reads were aligned to the Arabidopsis reference genome (TAIR10) using HISAT2. StringTie2 was used to count the reads numbers mapped to each gene and the R package DESeq2was used for differential expression analysis. The principal component analysis (PCA) and Pearson correlation were analyzed by the in-house R Script. All experiments were performed in three biological replicates.

2024-04-18 | E-MTAB-13956 | biostudies-arrayexpress

RNA sequencing of human esophageal myofibroblasts

Project description:We report the effect of treatment of primary cultures of human esophageal myofibroblasts with acidic bile salts

2022-09-28 | GSE197318 | GEO

Bile-induced biofilm formation in Bacteroides thetaiotaomicron requires magnesium efflux by an RND pump

Project description:The study is about the role of Bacteroides thetaiotaomicron in the human gut microbiota, specifically its ability to form biofilms in response to bile salts. The study found that bile induces the expression of certain efflux pumps, and inhibiting these pumps impairs biofilm formation. Among the induced pumps, the BipABC pump is crucial for biofilm formation as it is involved in the efflux of magnesium, which affects the biofilm's extracellular matrix and structure. This discovery sheds light on how intestinal chemical cues, like bile salts, regulate biofilm formation in B. thetaiotaomicron, a significant gut symbiont.

2024-03-19 | E-MTAB-13460 | biostudies-arrayexpress

Bile salts in Acinetobacter baumannii clinical strains with lack of AdeABC efflux pump

Project description:Few are the studies that analyzed the molecular features implicated to the tolerance to bile salts by A.baumannii clinical strains. Interestingly, Ab421 GEIH-2010 strain (belonging to ST79/PFGE-HUI-1 clone constitute by isolates with lacking of the AdeABC efflux pump) and A.baumannii ∆adeB ATCC 17978 showed higher tolerance to bile salts by the expression of the glutamate/aspartate transporter as well as virulence factors (Type VI Secretion System, twitching motility and biofilm) associated to the activation of the Quorum Sensing system.

2017-06-09 | GSE85264 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data